This is the order I have my hives in (I make all my own equipment by the way):
First is the hive stand, then comes the screened bottom board (I made mine with a slot below the screen to slide in a solid board to close them up in winter. You can also use the solid slide in board with a sticky sheet or vasoline to do a mite drop count. My solid slide in board stays out all summer.) The screened bottom board pictured above does not have a slot for the solid slide in board by the way. I do not use slatted racks, I find them to be redundant with the screened bottom board (not all will agree with me). Next comes the brood nest. I use all medium boxes (3 mediums in leau of 2 deeps here in the northeast). This allows me interchangability in all my equipment. If I need to borrow a frame of brood from a strong hive to bolster a weak hive, everything is in medium boxes. If I need to steal a frame of honey to feed a starving colony, everything is in medium boxes. Pull it out of one, put it in another! Mediums are by far easier to lift by the way! Next comes the honey supers. As stated before, all mediums. Then inner cover, popsicle sticks for upper ventilation, then outter cover. I do use an Imire shim from time to time over the brood nest when introducing a new queen or feeding pollen patties. I hope this helps. :D